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In particular the last part of your reply "but I shouldn't have to repeat really hard won battles again and again." is exactly what I meant when I posted the topic! And that´s what is still there to some extent with the Space Pirates at least in the room with the Dark Portal. I could finish them all off, and come back a minute later, and they´d be backk! For goodness and reality´s sake, nobody can replenish their ranks that quickly! It is too much and I do hope that they change it in the future. Killing enemies, doesn´t mean that there can´t be MORE coming. But it should be made more realistic in the way it´s being coded! Also the Chozo Ghosts that just kept coming back and back, made you wonder how many there are totally! 6 or 600? It gives a good feeling that you can go back to a room where you experience that the enemies you killed are dead, and not coming back again like your mega effort din´t have any impact. Otherwise it´s like Retro is mocking you!
A *really hard* battle is a boss, not some Chozo Ghosts or Space Pirates.
As for Metroid Prime 2:
Variability:
For example: The one area in Torvis Bogg that hosts the bridge to the EC. That room in particular had 4 different types of enemies at different times of visit. It settles in on one particular type later on, but it can also be completely void. Another example is the ship of the human commandos... sometimes it'll be a group of space pirates instead of war wasps. Also, when there are space pirates, they always grunt or have some kind of "I'm here" warning (most of the enemies do) and won't attack until you make yourself plainly available (by firing or running into plain sight). If for whatever reason you didn't want to face them, you could always make an about face, hit your map and figure out your options b/c of the....
I was just here 2 seconds ago rule:
In MP2: *If* you dispose of enemies in a room, then advance to the next room... The enemies will not return if you should you return to the original room. (Save for a few exceptions I'm sure) This helps for the all popular, "oh c*** wrong way/door"

Of course if you blew by them in the previous room... well you'll have a fun greeting at the door should you backtrack.
Rules of Engagement:
At no point am I forced to engage except for the "mini-bosses" such as
the dark pirate commandos... they appear as a set and you must fight them or "wait and hide, usually via morphball somewhere in the room". Encounters with dark pirate commandos are not mandatory otherwise!. If I were forced to clear out a room each time before advancing... *then* it becomes anoying.
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Make it varied how and where they re-appear, Retro, if so, and preferably make it more understood why it is possible that they can come back. Alternatively, make other enemies come to the same rooms, say, accompanied with a cutscene showing the moment you go back to that room, and the player will be more comfortable with having to fight again in a room he or she is passing through on the way to some other place. Instead oof making the person feel a need to scramble through just to make it out alive onto the real important destination!
Well, sans for the cut scenes *on each occurrence*, they pretty much have already done this, check out my examples above. Usually they seem to reserve cut scenes for when your already in a room and more enemies arrive. Which is good and preferable in my opinion.
Most of the time the enemies in MP2 have more reason for them coming back than other games... (Space Pirates are the plentiful enemy). Other enemies that are say dormant and embedded in the walls ... cough
IngSmasher, have a limited predefined number.
Personally I think they did an excellent job and handle it better than any other game out there.